DNA sequence elements required for transcription initiation of the Schizosaccharomyces pombe ADH gene in Saccharomyces cerevisiae

Furter‐Graves, Elizabeth M.; Hall, Benjamin D.

doi:10.1007/bf00264447

Cited by 46 publications

(44 citation statements)

References 42 publications

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“…Importance of a pyrimidine-purine sequence at the start site It is known that prokaryotic and other eukaryotic RNA polymerases generally use a purine as the starting nucleotide of transcripts (18)(19)(20)(21) and there are indications that this may also be true for Pol III (22,23). In all of our CSE spacing mutants the initiation site nucleotide was a purine preceded by a pyrimidine.…”

Section: Introductionmentioning

confidence: 80%

Mutational analysis of the transcription start site of the yeast tRNA^Leu₃gene

et al. 1995

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In addition to the well-known internal promoter elements of tRNA genes, 5' flanking sequences can also influence the efficiency of transcription by Saccharomyces cerevilsae extracts in vitro. A consensus sequence of yeast tRNA genes in the vicinity of the transcriptional start site can be derived. To determine whether the activity of this region can be attributed to particular sequence features we studied in vitro mutants of the start site region. We found that the start site can be shifted, but only to a limited extent, by moving the conserved sequence element. We found that both a pyrimidine-purine motif (with transcription initiating at the purine) and a small T:A base pair block upstream are important for efficient transcription in vitro. Thus the sequence surrounding the start site of transcription of the yeast tRNAL1u3 gene does play a role in determining transcription efficiency and fixing the precise site of initiation by RNA polymerase Ill.

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Section: Introductionmentioning

confidence: 80%

Mutational analysis of the transcription start site of the yeast tRNA^Leu₃gene

et al. 1995

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“…6). Examination of the sequence of the ADH1 and HIS3 start sites revealed that the ADH1 Ϫ38 and Ϫ37 sites and the ADH1 Ϫ28 and Ϫ27 sites reside within a CAAGC motif while the HIS3 Ϫ23 site is contained within the sequence CAGGC, both sharing homology with a PyAA/TPu proposed consensus sequence for S. cerevisiae RNAPII start sites (14,20,22). The suggestion that the differential sensitivity of these start sites to TFIIB mutations is due to sequence differences in the immediate vicinity of the sites was further supported by the demonstration that a T(Ϫ40)C substitution conferred decreased sensitivity of the ADH1 Ϫ38 and Ϫ37 sites to TFIIB mutations, whereas a G(Ϫ25)T substitution rendered the HIS3 Ϫ23 start site more sensitive (Fig.…”

Section: Discussionmentioning

confidence: 99%

Promoter-Specific Shifts in Transcription Initiation Conferred by Yeast TFIIB Mutations Are Determined by the Sequence in the Immediate Vicinity of the Start Sites

Faitar

Brodie

Ponticelli

2001

Molecular and Cellular Biology

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The general transcription factor IIB (TFIIB) is required for transcription of class II genes by RNA polymerase II. Previous studies demonstrated that mutations in the Saccharomyces cerevisiae SUA7 gene, which encodes TFIIB, can alter transcription initiation patterns in vivo. To further delineate the functional domain and residues of TFIIB involved in transcription start site utilization, a genetic selection was used to isolate S. cerevisiae TFIIB mutants exhibiting downstream shifts in transcription initiation in vivo. Both dominant and recessive mutations conferring downstream shifts were identified at multiple positions within a highly conserved homology block in the N-terminal region of the protein. The TFIIB mutations conferred downstream shifts in transcription initiation at the ADH1 and CYC1 promoters, whereas no significant shifts were observed at the HIS3 promoter. Analysis of a series of ADH1-HIS3 hybrid promoters and variant ADH1 and HIS3 promoters containing insertions, deletions, or site-directed base substitutions revealed that the feature that renders a promoter sensitive to TFIIB mutations is the sequence in the immediate vicinity of the normal start sites. We discuss these results in light of possible models for the mechanism of start site utilization by S. cerevisiae RNA polymerase II and the role played by TFIIB.Accurate and efficient transcription of eukaryotic proteincoding (class II) genes involves the concerted action of RNA polymerase II (RNAPII) and a host of accessory proteins. A subset of these proteins are known as the general transcription factors (GTFs) and include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH (reviewed in reference 34). The GTFs are being intensively studied with the objective of determining their respective functions during the different stages of RNAPII transcription, which include (i) formation of a preinitiation complex (PIC) on the promoter, (ii) melting of the promoter DNA, (iii) transcription initiation, (iv) clearance of RNAPII from the promoter, (v) elongation of the nascent transcript, and (vi) transcription termination.Most promoters of class II genes contain both upstream regulatory elements and TATA elements. TATA elements, containing the consensus sequence TATAa/tAa/t, are located upstream of the mRNA start sites and are specific binding sites for the TATA-binding protein (TBP) subunit of TFIID (32, 36). For most class II promoters, formation of an active PIC is thought to occur by the initial binding of TFIID to the TATA element, in some cases accompanied by TFIIA. It is proposed that PIC formation then proceeds by either an ordered stepwise association of the remaining factors and RNAPII or by the direct recruitment of RNAPII holoenzyme (reviewed in reference 34). Upon PIC formation, the promoter DNA can be melted in an energy-dependent step, facilitating the initiation of mRNA synthesis and clearance of RNAPII from the promoter. In higher eukaryotes, transcription initiation usually occurs at a discrete start site located about 25 to 30 bp downstrea...

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“…The initial sequence comparisons and mutational analysis of a relatively small set of yeast mRNA genes helped define three related yeast start site consensus sequences, RRYRR, TCRA, and YA(A/T)R in the non-template strand, where the initiation site is underlined, Y is pyrimidine, and R is purine (12)(13)(14). Recently, an alignment of sequences flanking 4637 yeast transcription start sites has provided a more refined consensus sequence: A(A rich ) 5 NYA(A/T)NN(A rich ) 6 (15).…”

Section: Eukaryotes Rely On Rna Polymerase II (Rnap Ii)mentioning

confidence: 99%

Quantitative Analysis of in Vivo Initiator Selection by Yeast RNA Polymerase II Supports a Scanning Model

Kuehner

Brow

2006

Journal of Biological Chemistry

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Initiation of transcription by RNA polymerase II (RNAP II) onSaccharomyces cerevisiae messenger RNA (mRNA) genes typically occurs at multiple sites 40 -120 bp downstream of the TATA box. The mechanism that accommodates this extended and variable promoter architecture is unknown, but one model suggests that RNAP II forms an open promoter complex near the TATA box and then scans the template DNA strand for start sites. Unlike most proteincoding genes, small nuclear RNA gene transcription starts predominantly at a single position. We identify a highly efficient initiator element as the primary start site determinant for the yeast U4 small nuclear RNA gene, SNR14. Consistent with the scanning model, transcription of an SNR14 allele with tandemly duplicated start sites initiates primarily from the upstream site, yet the downstream site is recognized with equivalent efficiency by the diminished population of RNAP II molecules that encounter it. A quantitative in vivo assay revealed that SNR14 initiator efficiency is nearly perfect (ϳ90%), which explains the precision of U4 RNA 5 end formation. Initiator efficiency was reduced by cis-acting mutations at ؊8, ؊7, ؊1, and ؉1 and trans-acting substitutions in the TFIIB B-finger. These results expand our understanding of RNAP II initiation preferences and provide new support for the scanning model. Eukaryotes rely on RNA polymerase II (RNAP II)2 to synthesize all messenger RNAs (mRNAs) and most of the small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) encoded within their nuclear genomes. Efficient and accurate transcription initiation is vital to ensure the proper expression and function of these RNAs. The recruitment of RNAP II to gene promoters is mediated through the assembly of a pre-initiation complex (PIC). RNAP II accessory proteins provide promoter specificity and the structural core for assembly of the PIC. These accessory proteins include the general transcription factors TFIID, TFIIB, TFIIF, TFIIE, and TFIIH (1-3). Some transcription factors engage in sequence-specific contacts with core promoter elements (4); one of the most fundamental interactions for PIC assembly is between the TATA-binding protein subunit of TFIID and the TATA box (5-6). In a stepwise model for PIC assembly, TATA-binding protein binding is followed by the addition of TFIIB, RNAP II-TFIIF, TFIIE, and TFIIH (7).In metazoans, the assembly of a PIC at the TATA box results in start site selection 25-30 bp downstream (4). The architecture of the PIC is such that the transcription start site is placed precisely within the active center of RNAP II (8 -9). In the yeast Saccharomyces cerevisiae, RNAP II initiation typically occurs at multiple sites at variable distances from the TATA box, with most start sites ranging from 40 to 120 bp downstream of the TATA box (10). The initiation mechanism that accommodates this extended and variable promoter architecture is unknown, but it does not appear to be dependent on assembling the yeast PIC in a manner different from that of metazoans. Yeast p...

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DNA sequence elements required for transcription initiation of the Schizosaccharomyces pombe ADH gene in Saccharomyces cerevisiae

Cited by 46 publications

References 42 publications

Mutational analysis of the transcription start site of the yeast tRNA^Leu₃gene

Mutational analysis of the transcription start site of the yeast tRNA^Leu₃gene

Promoter-Specific Shifts in Transcription Initiation Conferred by Yeast TFIIB Mutations Are Determined by the Sequence in the Immediate Vicinity of the Start Sites

Quantitative Analysis of in Vivo Initiator Selection by Yeast RNA Polymerase II Supports a Scanning Model

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DNA sequence elements required for transcription initiation of the Schizosaccharomyces pombe ADH gene in Saccharomyces cerevisiae

Cited by 46 publications

References 42 publications

Mutational analysis of the transcription start site of the yeast tRNALeu3gene

Mutational analysis of the transcription start site of the yeast tRNALeu3gene

Promoter-Specific Shifts in Transcription Initiation Conferred by Yeast TFIIB Mutations Are Determined by the Sequence in the Immediate Vicinity of the Start Sites

Quantitative Analysis of in Vivo Initiator Selection by Yeast RNA Polymerase II Supports a Scanning Model

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Mutational analysis of the transcription start site of the yeast tRNA^Leu₃gene

Mutational analysis of the transcription start site of the yeast tRNA^Leu₃gene